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release_v1.6.md

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MagellanMapper v1.6 Release Notes

MagellanMapper v1.6.0

Highlights

Changes

Installation

GUI

  • More preferences are saved, such as the figure save location and ROI Editor layout (#138)
  • "Blend" option in the image adjustment panel to visualize alignment in overlaid images
  • Drag and remove loaded profiles in the Profiles tab table
  • "Help" buttons added to open the online documentation (#109)
  • Default confirmation labels can be set before detection (#115)
  • Resets the labels reference file path when reloading an image in the GUI (#139)
  • BrainGlobe panel: access atlases hosted by BrainGlobe directly from the GUI (#75)
  • Registered image suffixes with variable endings (eg annotationEdgeLevel<n>) now show up in the dropdown boxes (#142)
  • Registered image and region names are truncated in the middle to prevent expanding the sidebar for long names (#147)
  • "Show all" in the Regions section of the ROI panel shows names for all labels (#145)
  • Fixed to reset the ROI selector when redrawing (#115)
  • Fixed to reorient the camera after clearing the 3D space (#121)
  • Fixed to turn off the minimum intensity slider's auto setting when manually changing the slider (#126)
  • Fixed error window when moving the atlas level slider before a 3D image has been rendered (#139)
  • Fixed saving blobs in an ROI using the first displayed ROI or after moving the sliders without redrawing (#139)
  • Fixed synchronization between the ROI Editor and image adjustment controls after initialization (#142)

CLI

  • The --proc export_tif task exports an NPY file to TIF format
  • the --transform interpolation=<n> configures the type of interpolation when resizing images during stack export (#127)
  • Any axis can be flipped through --transform flip=<axis>, where axis = 0 for the z-axis, 1 for the y-axis, and 2 for the x-axis (#147)
  • Density/heat maps can be specified through --reg_suffixes density=<suffix> (#129)
  • Fixed to only remove the final extension from image paths, and paths given by the --prefix <path> CLI argument do not undergo any stripping (#115)

Atlas refinement

Atlas registration

  • Image registration now supports multiple labels images given as --reg_suffixes annotation=<suffix1>,<suffix2>,..., which will apply the same transformation to each of these images (#147)
  • Landmark distance measurements save the raw distances and no longer require spacing (#147)

Cell detection

Detection
  • Detection channels can be selected, including those not in the currently displayed image or loaded from a saved blobs file (#121)
  • Auto-scrolls the detections table to the selected annotation (#109)
  • ctrl+[n]+click to add a channel now sets the channel directly to n rather than to the nth seleted channel (#109)
  • Added a slider to choose the fraction of 3D blobs to display (#121)
  • Improved blob size slider range and readability (#121)
  • Blob columns can be customized, including excluding or reordering columns (#133)
  • Fixed to scale blobs' radii when viewing blobs detections on a downsampled image (#121)
  • Fixed getting atlas colors for blobs for ROIs inside the main image (#121)
  • Fixed blob segmentation for newer versions of Scikit-image (#91)
  • Fixed verifying and resaving blobs
Colocalization
  • Match-based colocalization can run without the main image, using just its metadata instead (#117)
  • These colocalizations are now displayed in the 3D viewer (#121)
  • Fixed match-based colocalizations when no matches are found (#117, #120)
  • Fixed slow loading of match-based colocalizations (#119, #123)

Volumetric image processing

  • Match-based colocalizations use larger processing blocks to avoid gaps (#120)
  • Voxel density maps no longer require a registered image (#125)
  • Grid search profiles are now layered on top of one another rather than applied in sequential runs for consistency with ROI and atlas profiles (#138)
  • Fixed 3D surface area measurement with Scikit-image >= v0.19

I/O

  • Images can be viewed as RGB(A) using the RGB button or the --rgb CLI argument (#142)
  • Some TIF files can be loaded directly, without importing the file first (#90)
  • The --proc export_planes task can export a subset of image planes specified by --slice, or an ROI specified by --offset and --size
  • Image metadata is stored in the Image5d image object (#115)
  • Better 2D image support
    • Extended zero-crossing detection to 2D cases (#142)
    • Unit factor conversions adapts to image dimensions (eg 2D vs 3D) (#132)
  • Fixed re-importing an image after loading it (#117)
  • Fixed to store the image path when loading a registered image as the main image, which fixes saving the experiment name used when saving blobs (#139)

Server pipelines

Python stats and plots

  • Generate swarm plots in Seaborn (#137)
  • Color bars can be configured in ROI profiles using settings in Matplotlib, update dynamically, and no longer repeat in animations (#128)
  • New plot label sub-arguments (#135):
    • --plot labels err_col_abs=<col>: plot error bars with a column of absolute rather than relative values, now that Clrstats gives absolute values for effect sizes
    • --plot_labels background=<color>: change plot background color with a Matplotlib color string
    • --plot_labels vspan_col=<col> vspan_format=<str>: column denoting vertical span groups and string format for them, respectively (#135, 137)
  • Fixed errors when generating labels difference heat maps, and conditions can be set through --plot_labels condition=cond1,cond2,... (#132)
  • Fixed alignment of headers and columns in data frames printed to console (#109)

R stats and plots

  • Specify models with the --model <stats.model> CLI argument (#135)
  • Effect size confidence intervals are now absolute rather than relative values for clarity (#135)
  • Region IDs file is no longer required since volume stats output from the Python pipeline already includes this region metadata (#132)
  • Added the diff.means stats model to simply give the difference of means between conditions (#135)
  • The revpairedstats profile is now revconds since it applies to reversing conditions in general, not just for paired stats (#132)
  • Stats errors are caught rather than stopping the pipeline (#132)
  • The labels reference path has been moved to an environment variable, which can be configured through --labels <path> (#147)
  • The Shapiro-Wilks test has been implemented in meansModel for consistent table output (#164)
  • Fixed t-test, which also provides Cohen's d as a standardized effect size through the effectsize package (#135)
  • Fixed jitter plot box plots to avoid covering labels (#147)

Code base and docs

  • Blob column accessors are encapsulated in the Blobs class, which allows for flexibility in column inclusion and order (#133)
  • Settings profiles are being migrated from dictionaries to data classes to document and configure settings more easily (#138)

Dependency Updates

Python Dependency Changes

  • Python 3.8 is the default version now that Python 3.6 has reached End-of-Life
  • The BrainGlobe Atlas API package (bg-atlasapi) dependency has been added to access a suite of cloud-based atlases (#75)
  • The dataclasses backport is installed for Python < 3.7
  • Tifffile is now a direct dependency, previously already installed as a sub-dependency of other required packages
  • Imagecodecs is optional for tifffile but required for its uses here as of tifffile v2022.7.28 and thus added as a dependency (#153)
  • Updated to use the axis_channel parameter in Scikit-image's transform.rescale function (#115)
  • Seaborn as an optional dependency for additional plot support (currently only swarm plots, #137)
  • Scikit-learn is an optional rather than a required dependency (#150)
  • The AWS-related dependencies (boto3, awscli) are also no longer installed in Conda environments (#150)

R Dependency Changes

  • effectsize is a suggested dependency for Cohen's d, used in t-tests (#135)

Server dependency Changes